void pike_module_init( void )
{
STRS(data) = make_shared_string("data");
STRS(file) = make_shared_string("file");
STRS(method) = make_shared_string("method");
STRS(protocol) = make_shared_string("protocol");
STRS(query) = make_shared_string("query");
STRS(raw_url) = make_shared_string("raw_url");
SVAL(data)->type = T_STRING;
SVAL(file)->type = T_STRING;
SVAL(method)->type = T_STRING;
SVAL(protocol)->type = T_STRING;
SVAL(query)->type = T_STRING;
SVAL(raw_url)->type = T_STRING;
add_function_constant( "parse_headers", f_parse_headers,
"function(string:mapping)", 0);
add_function_constant( "parse_query_string", f_parse_query_string,
"function(string,mapping:void)",
OPT_SIDE_EFFECT);
add_function_constant( "get_address", f_get_address,
"function(string:string)", 0);
start_new_program();
ADD_STORAGE( buffer );
add_function( "append", f_buf_append,
"function(string:int)", OPT_SIDE_EFFECT );
add_function( "create", f_buf_create, "function(mapping,mapping:void)", 0 );
set_exit_callback(free_buf_struct);
set_init_callback(alloc_buf_struct);
parsehttp_program = end_program();
add_program_constant("ParseHTTP", parsehttp_program, 0);
}
struct arc *leaf_to_arc (struct leaf *lf)
{
int j, k;
struct arc *a;
struct vertex *v;
struct cept *ex;
a = allocate_arc ();
if (a == NULL) {
add_object (tail_cept, ARC, "leaf arc");
add_function (tail_cept, "leaf_to_arc");
add_source (tail_cept, "msrender.c");
return(NULL);
}
a -> cir = lf -> cir;
for (j = 0; j < 2; j++) {
v = allocate_vertex ();
if (error()) {
add_object (tail_cept, VERTEX, "leaf vertex");
add_function (tail_cept, "leaf_to_arc");
add_source (tail_cept, "msrender.c");
return(NULL);
}
for (k = 0; k < 3; k++)
v -> center[k] = lf -> ends[j][k];
a -> vtx[j] = v;
}
return (a);
}
int closest (struct surface *current_surface, struct leaf *lf, double pnt[3])
{
int j, k, jmin, nch;
double dmin;
double dta[MAXPA];
double several_centers[MAXPA][3], several_radii[MAXPA];
struct cept *ex;
if (lf -> type == SPHERE && lf -> shape == CONVEX) nch = 1;
else if (lf -> shape == SADDLE) nch = 2;
else if (lf -> type == SPHERE && lf -> shape == CONCAVE) nch = 3;
else if (lf -> type == CYLINDER) nch = 2;
else if (lf -> type == TORUS && lf -> shape == CONVEX) nch = 1;
else {
ex = new_cept (LOGIC_ERROR, NOT_FOUND, FATAL_SEVERITY);
add_function (ex, "closest");
add_source (ex, "msrender.c");
add_long (ex, "leaf type", (long) lf -> type);
add_long (ex, "leaf shape", (long) lf -> shape);
return(0);
}
if (nch <= 1)
return (lf -> atmnum[0]);
if (lf -> atmnum[3] > 0)
nch = 4;
for (j = 0; j < nch; j++) {
for (k = 0; k < 3; k++)
several_centers[j][k] = *(current_surface -> atom_centers + 3 * (lf -> atmnum[j] - 1) + k);
several_radii[j] = *(current_surface -> atom_radii + (lf -> atmnum[j] - 1));
}
/* find closest atom */
for (j = 0; j < nch; j++)
dta[j] = distance (pnt, several_centers[j]) - several_radii[j];
/* initialization */
dmin = 1000000.0;
jmin = -1;
for (j = 0; j < nch; j++)
if (dta[j] < dmin) {
dmin = dta[j];
jmin = j;
}
if (jmin < 0 || jmin >= nch) {
ex = new_cept (LOGIC_ERROR, NOT_FOUND, FATAL_SEVERITY);
add_function (ex, "closest");
add_source (ex, "msrender.c");
add_message (ex, "cannot find closest atom");
return (0);
}
return (lf -> atmnum[jmin]);
}
/* create permanent tori */
void create_permanent (struct surface *this_srf)
{
int k;
long niter;
char message[MAXLINE];
struct arc *arcptr;
struct torus *torus_ptr;
struct central *central_ptr;
struct cept *ex;
/* create permanent tori for central circles */
this_srf -> n_tori = 0;
if (this_srf -> n_pair > 0) {
for (central_ptr = this_srf -> head_central; central_ptr != NULL;
central_ptr = central_ptr -> next) {
torus_ptr = allocate_torus ();
if (torus_ptr == NULL) {
ex = new_cept (MEMORY_ERROR, ALLOCATION, FATAL_SEVERITY);
add_object (ex, TORUS, "torus");
add_function (ex, "create_permanent");
add_source (ex, "mstorus.c");
return;
}
/* store data in structure */
for (k = 0; k < 3; k++) {
torus_ptr -> center[k] = central_ptr -> center[k];
torus_ptr -> axis[k] = central_ptr -> axis[k];
}
torus_ptr -> radius = central_ptr -> radius;
torus_ptr -> atm[0] = central_ptr -> sph[0];
torus_ptr -> atm[1] = central_ptr -> sph[1];
torus_ptr -> free = central_ptr -> free;
torus_ptr -> buried = 0;
torus_ptr -> first_arc = central_ptr -> first_arc;
/* set up arc -> torus pointers */
niter = 0;
for (arcptr = torus_ptr -> first_arc; arcptr != NULL;
arcptr = arcptr -> next, niter++) {
arcptr -> tor = torus_ptr;
if (niter > 2 * this_srf -> n_atom) {
add_object (ex, ARC, "arcptr");
add_function (ex, "create_permanent");
add_source (ex, "mstorus.c");
add_message (ex, "infinite loop for torus <--> arc");
return;
}
}
if (this_srf -> head_torus == NULL) this_srf -> head_torus = torus_ptr;
else this_srf -> tail_torus -> next = torus_ptr;
this_srf -> tail_torus = torus_ptr;
this_srf -> n_tori++;
torus_ptr -> number = this_srf -> n_tori;
}
}
sprintf (message,"%8ld tori", this_srf -> n_tori); inform(message);
}
int subdivide_leaf (double fine_pixel, struct leaf *lf, double **pntptr)
{
int j, k, n;
double alpha;
struct arc *lfarc;
struct vertex *lfvtx[2];
struct cept *ex;
if (lf -> cir -> radius <= 0.0) {
return (0);
}
lfarc = allocate_arc ();
if (lfarc == NULL) {
add_object (tail_cept, ARC, "leaf arc");
add_function (tail_cept, "subdivide_leaf");
add_source (tail_cept, "msrender.c");
return (0);
}
for (j = 0; j < 2; j++) {
lfvtx[j] = allocate_vertex ();
if (error()) {
add_object (tail_cept, VERTEX, "leaf vertex");
add_function (tail_cept, "subdivide_leaf");
add_source (tail_cept, "msrender.c");
return (0);
}
}
/* convert to arc for subdivision */
lfarc -> cir = lf -> cir;
for (k = 0; k < 3; k++) {
lfvtx[0] -> center[k] = lf -> ends[0][k];
lfvtx[1] -> center[k] = lf -> ends[1][k];
}
for (j = 0; j < 2; j++)
lfarc -> vtx[j] = lfvtx[j];
/* angular parameter for subdivision */
alpha = fine_pixel / (lf -> cir -> radius);
/* call geometric subdivision function */
n = render_sub_arc (lfarc, pntptr, alpha);
if (error()) return(0);
free_arc (lfarc);
for (j = 0; j < 2; j++)
free_vertex (lfvtx[j]);
return (n); /* return number of subdivision points */
}
void def(std::string const &name, R (*f)(BOOST_PP_ENUM_PARAMS(n,T)),
policies const &p = policies())
{
add_function(name,
boost::shared_ptr<details::callback_base>(
new details::BOOST_PP_CAT(callback,n)<R BOOST_PP_COMMA_IF(n) BOOST_PP_ENUM_PARAMS(n,T)>(f)), p);
}
std::unique_ptr<graphics::plot> create_function_plot(const char *title, unsigned flags) {
auto p = std::make_unique<graphics::plot>(graphics::plot::show_units | graphics::plot::auto_limits);
p->set_clip_mode(false);
p->set_title(title);
agg::rgba8 blue(0, 0, 180, 255);
agg::rgba8 red(180, 0, 0, 255);
const double x0 = 3.14159265358979323846/2, x1 = 8 * 2 * 3.14159265358979323846;
auto fsin = [](double x) { return std::sin(x) / x; };
auto fcos = [](double x) { return std::cos(x) / x; };
add_function(*p, x0, x1, fsin, blue, flags);
add_function(*p, x0, x1, fcos, red, flags);
p->commit_pending_draw();
return p;
}
void add_function(const std::string &name,
const std::string &source,
const std::map<std::string, std::string> &definitions)
{
typedef std::map<std::string, std::string>::const_iterator iter;
std::stringstream s;
// add #define's
for(iter i = definitions.begin(); i != definitions.end(); i++){
s << "#define " << i->first;
if(!i->second.empty()){
s << " " << i->second;
}
s << "\n";
}
s << source << "\n";
// add #undef's
for(iter i = definitions.begin(); i != definitions.end(); i++){
s << "#undef " << i->first << "\n";
}
add_function(name, s.str());
}
int along (struct edge *edg, double axis[3])
{
int orn, k, sgn;
double dt;
double vect[3];
struct vertex *vtx1, *vtx2;
struct arc *a;
struct cept *ex;
a = edg -> arcptr;
vtx1 = a -> vtx[0];
vtx2 = a -> vtx[1];
if (vtx1 == NULL || vtx2 == NULL) {
ex = new_cept (PARAMETER_ERROR, NULL_VALUE, FATAL_SEVERITY);
add_object (ex, VERTEX, "vtx1 or vtx2");
add_function (ex, "along");
add_source (ex, "msrender.c");
return(0);
}
orn = edg -> orn;
sgn = 1 - 2 * orn;
for (k = 0; k < 3; k++)
vect[k] = vtx2 -> center[k] - vtx1 -> center[k];
dt = dot_product (vect, axis) * sgn;
return (dt > 0.0);
}
bool check_prog(struct prog* prog, struct symtable *syms)
{
bool correct = true;
fill_std_types(syms);
fill_std_fun(syms);
constdecllist_t consts = prog->entry_point->const_decls;
for(unsigned i =0; i < consts.size; ++i)
correct = correct && check_const(list_nth(consts,i), syms, true);
correct = correct && add_types(syms, prog->entry_point->type_decls);
correct = correct && add_variables(syms, prog->entry_point->var_decl, true, false, false);
for(unsigned i = 0; i < prog->algos.size; ++i)
{
struct algo* al = list_nth(prog->algos, i);
struct function* f = malloc(sizeof(struct function));
f->ident = al->ident;
f->ret = find_type(syms->types, al->return_type);
f->arg = get_args(al->declarations->param_decl, syms);
add_function(syms->functions, f);
}
for (unsigned i = 0; i < prog->entry_point->instructions.size; ++i)
if (!check_inst(
prog->entry_point->instructions.data[i],
find_type(syms->types, TYPE_INT), syms))
correct = false;
for(unsigned i = 0; i < prog->algos.size; ++i)
{
struct algo* al = list_nth(prog->algos, i);
if (!check_algo(al, syms))
correct = false;
}
return correct;
}
void compute_torus_center (double probe_radius, struct sphere *sphere1,struct sphere *sphere2, double torus_center[3])
{
int k;
double radius1, radius2, asymmetry, distance12_squared;
char message[MAXLINE];
struct cept *ex;
distance12_squared =
distance_squared (sphere1 -> center, sphere2 -> center);
if (distance12_squared <= 0.0) {
ex = new_cept (GEOMETRY_ERROR, DEGENERACY, FATAL_SEVERITY);
add_function (ex, "compute_torus_center");
add_source (ex, "mstorus.c");
add_message (ex, "coincident atoms");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
return;
}
radius1 = sphere1 -> radius;
radius2 = sphere2 -> radius;
asymmetry = (radius1 + probe_radius) * (radius1 + probe_radius) -
(radius2 + probe_radius) * (radius2 + probe_radius);
for (k = 0; k < 3; k++)
torus_center[k] = 0.5 * (sphere1 -> center[k] + sphere2 -> center[k])
+ 0.5 * ( asymmetry / distance12_squared) *
(sphere2 -> center[k] - sphere1 -> center[k]);
}
VariableMap::VariableMap( int function_count, std::vector<bool> common )
: input_var_c(common.size()), output_var_c(0)
{
for (int i = 0; i < function_count; ++i) {
add_function( common );
}
}
/**
* Increment of a given key, by number $value
*
* @param string $keyName
* @param long $value
* @return mixed
*/
PHP_METHOD(Phalcon_Cache_Backend_Apc, increment){
zval *key_name, *value = NULL, prefix = {}, prefixed_key = {}, cached_content = {};
phalcon_fetch_params(0, 1, 1, &key_name, &value);
if (!value || Z_TYPE_P(value) == IS_NULL) {
value = &PHALCON_GLOBAL(z_one);
} else {
PHALCON_ENSURE_IS_LONG(value);
}
phalcon_read_property(&prefix, getThis(), SL("_prefix"), PH_NOISY);
PHALCON_CONCAT_SVV(&prefixed_key, "_PHCA", &prefix, key_name);
phalcon_update_property_zval(getThis(), SL("_lastKey"), &prefixed_key);
if (SUCCESS == phalcon_function_exists_ex(SL("apc_inc"))) {
PHALCON_RETURN_CALL_FUNCTIONW("apc_inc", &prefixed_key, value);
} else {
PHALCON_CALL_FUNCTIONW(&cached_content, "apc_fetch", &prefixed_key);
if (Z_TYPE(cached_content) == IS_LONG) {
add_function(return_value, &cached_content, value);
PHALCON_CALL_METHODW(NULL, getThis(), "save", key_name, return_value);
} else {
RETURN_FALSE;
}
}
}
void litehtml::el_before_after_base::add_style(const litehtml::style& st)
{
html_tag::add_style(st);
tstring content = get_style_property(_t("content"), false, _t(""));
if(!content.empty())
{
int idx = value_index(content.c_str(), content_property_string);
if(idx < 0)
{
tstring fnc;
tstring::size_type i = 0;
while(i < content.length() && i != tstring::npos)
{
if(content.at(i) == _t('"'))
{
fnc.clear();
i++;
tstring::size_type pos = content.find(_t('"'), i);
tstring txt;
if(pos == tstring::npos)
{
txt = content.substr(i);
i = tstring::npos;
} else
{
txt = content.substr(i, pos - i);
i = pos + 1;
}
add_text(txt);
} else if(content.at(i) == _t('('))
{
i++;
litehtml::trim(fnc);
litehtml::lcase(fnc);
tstring::size_type pos = content.find(_t(')'), i);
tstring params;
if(pos == tstring::npos)
{
params = content.substr(i);
i = tstring::npos;
} else
{
params = content.substr(i, pos - i);
i = pos + 1;
}
add_function(fnc, params);
fnc.clear();
} else
{
fnc += content.at(i);
i++;
}
}
}
}
}
/* write face */
void write_faces (struct surface *srf, FILE *fp_surface)
{
int icyc;
long n_face;
char message[MAXLINE];
struct face *fac;
struct facbin facout;
struct variety *vty;
struct cept *ex;
n_face = 0;
icyc = 1;
for (fac = srf -> head_face; fac != NULL; fac = fac -> next) {
vty = fac -> vty;
if (vty == NULL) {
ex = new_cept (POINTER_ERROR, NULL_VALUE, FATAL_SEVERITY);
add_function (ex, "write_faces");
add_source (ex, "msrollio.c");
return;
}
facout.error = 0;
facout.vtynum = vty -> number;
sprintf (message, "%8ld face %8ld variety %1d shape",
n_face, vty -> number, (int) fac -> shape);
informd (message);
switch ((int) fac -> shape) {
case CONVEX:
facout.type = CONVEX_FACE_TYPE;
facout.fcynum = ((fac -> n_cycle > 0) ? icyc : 0);
icyc += fac -> n_cycle;
break;
case SADDLE:
facout.type = SADDLE_FACE_TYPE;
facout.fcynum = icyc;
if (fac -> n_arc == 2) icyc += 2;
else icyc++;
break;
case CONCAVE:
facout.type = CONCAVE_FACE_TYPE;
/* problem concave face */
if (fac -> problem) facout.error = 1;
facout.fcynum = icyc;
if (fac -> ptr.prb -> low)
icyc += fac -> n_cycle;
else icyc++;
break;
default:
set_error1 ("write_faces: invalid face shape");
return;
}
facout.comp = fac -> comp;
fwrite ((char *) &facout, sizeof (facout), 1, fp_surface);
n_face++;
}
sprintf (message, "%8ld faces written", n_face);
informd (message);
}
Function *FunctionManager::build_function_internal(
uint16_t address, const uint8_t *ct_memory)
{
Registers ®isters = mpu_->internal->registers_;
TRACE("Building Function for code at 0x" << std::hex << std::setfill('0') <<
std::setw(4) << registers.pc);
FunctionBuilder fb(mpu_, ct_memory, code_at_address_, registers.pc);
boost::shared_ptr<Function> f(fb.build());
add_function(f);
return f.get();
}
/* Initialize and start module */
void pike_module_init( void )
{
STRS(data) = make_shared_string("data");
STRS(file) = make_shared_string("file");
STRS(method) = make_shared_string("method");
STRS(protocol) = make_shared_string("protocol");
STRS(query) = make_shared_string("query");
STRS(raw_url) = make_shared_string("raw_url");
SVAL(data)->type = T_STRING;
SVAL(file)->type = T_STRING;
SVAL(method)->type = T_STRING;
SVAL(protocol)->type = T_STRING;
SVAL(query)->type = T_STRING;
SVAL(raw_url)->type = T_STRING;
add_function_constant( "parse_headers", f_parse_headers,
"function(string:mapping)", 0);
add_function_constant( "parse_query_string", f_parse_query_string,
"function(string,mapping:void)",
OPT_SIDE_EFFECT);
add_function_constant( "parse_prestates", f_parse_prestates,
"function(string,multiset,multiset:string)",
OPT_SIDE_EFFECT);
add_function_constant( "get_address", f_get_address,
"function(string:string)", 0);
add_function_constant( "extension", f_extension,
"function(string:string)", 0);
add_function_constant( "create_process", f_create_process,
"function(array(string),void|mapping(string:mixed):int)", 0);
start_new_program();
ADD_STORAGE( buffer );
add_function( "append", f_buf_append,
"function(string:int)", OPT_SIDE_EFFECT );
add_function( "create", f_buf_create, "function(mapping,mapping,int|void:void)", 0 );
set_init_callback(alloc_buf_struct);
set_exit_callback(free_buf_struct);
end_class("ParseHTTP", 0);
init_nbio();
}
void translation_init(void)
{
add_function("lt", &eval_lt);
add_function("eq", &eval_eq);
add_function("int", &eval_int);
add_function("add", &eval_add);
add_function("strlen", &eval_strlen);
add_function("if", &eval_if);
add_function("isnull", &eval_isnull);
}
int
function_register(const function_t *func_info)
{
if(function_registered(func_info->name))
{
return 1;
}
if(add_function(func_info) != 0)
{
return 1;
}
return 0;
}
struct leaf *allocate_leaf ()
{
struct leaf *lef;
struct cept *ex;
lef = (struct leaf *) allocate_object (LEAF);
if (lef == NULL) {
ex = new_cept (MEMORY_ERROR, ALLOCATION, FATAL_SEVERITY);
add_function (ex, "allocate_leaf");
add_source (ex, "msrender.c");
return(NULL);
}
return (lef);
}
std::shared_ptr<soft_function> environment::find_or_add (const std::string& name)
{
auto func(find_function(name));
if (func == nullptr)
{
std::shared_ptr<soft_function> soft_func(new soft_function(name));
add_function(soft_func);
return soft_func;
}
else if (!func->is_native())
return std::static_pointer_cast<soft_function>(func);
else
return nullptr;
}
void init_avs_count_program(void)
{
// start building the AVS.Search program
start_new_program();
// request space for the per-object private data
ADD_STORAGE(struct private_count_data);
// add the program methods
add_function("create", f_create,
"function(object:void)", ID_PUBLIC);
add_function("destroy", f_destroy,
"function(void:void)", ID_PUBLIC);
add_function("get_count", f_get_count,
"function(void:int)", ID_PUBLIC);
add_function("next", f_next,
"function(void:void)", ID_PUBLIC);
add_function("get_word", f_get_word,
"function(void:string)", ID_PUBLIC);
// finish and add the AVS.Search program
count_program = end_program();
add_program_constant("Count", count_program, 0);
}
struct surface *new_surface ()
{
struct surface *srf_ptr;
struct cept *ex;
srf_ptr = (struct surface *) allocate_object (SURFACE);
if (srf_ptr == NULL) {
ex = new_cept (MEMORY_ERROR, ALLOCATION, FATAL_SEVERITY);
add_object (ex, SURFACE, "srf_ptr");
add_function (ex, "new_surface");
return (NULL);
}
srf_ptr -> surface_thickness = DEFAULT_THICKNESS;
return (srf_ptr);
}
static int add_functions_from_module(libcrange* lr, set* functions,
const char* module, const char* prefix)
{
void* handle;
char filename[512];
const char** all_functions;
snprintf(filename,
sizeof filename,
"%s/%s.so",
/* if absolute path, don't use funcdir
* bit of a hack. FIXME need better handling
* for setting funcdir and other implied paths
* in the conf
*/
module[0] == '/' ? "" : lr->funcdir,
module);
filename[sizeof filename - 1] = '\0';
if (access(filename, R_OK) != 0) {
fprintf(stderr, "module %s (can't read %s.)\n",
module, filename);
return 1;
}
if ((handle = dlopen(filename, RTLD_NOW)) == NULL) {
fprintf(stderr, "%s: can't dlopen: %s\n", filename, dlerror());
return 1;
}
dlerror(); /* Clear any existing errors */
all_functions = get_function_names(lr, handle, module);
if (all_functions == NULL)
return 1;
while (*all_functions) {
int err = add_function(lr, functions, handle,
module, prefix, *all_functions++);
if (err != 0)
return err;
}
return 0;
}
void render_surface (struct msscene *ms, struct surface *current_surface)
{
int is_vdw, type;
double fine_pixel;
char message[MAXLINE];
struct face *fac;
struct variety *vty;
struct cept *ex;
fine_pixel = ms -> pixel_width / ms -> fineness;
is_vdw = (current_surface -> type == PQMS_SURFACE && current_surface -> probe_radius <= 0.0);
for (fac = current_surface -> head_face; fac != NULL; fac = fac -> next) {
vty = fac -> vty;
if (fac -> problem) {
sprintf (message,"skip problem face of atoms %5d %5d %5d %5d",
vty -> atmnum[0], vty -> atmnum[1], vty -> atmnum[2], vty -> atmnum[3]);
inform(message);
continue;
}
if (is_vdw && (fac -> shape == CONCAVE || fac -> shape == SADDLE))
continue;
type = (int) vty -> type;
switch (type) {
case SPHERE:
slice_sphere (ms, current_surface, fine_pixel, fac);
break;
case TORUS:
slice_torus (ms, current_surface, fine_pixel, current_surface -> probe_radius, fac);
break;
case CYLINDER:
slice_cylinder (ms, current_surface, fine_pixel, fac);
break;
default:
ex = new_cept (ENUM_ERROR, INVALID_VALUE, FATAL_SEVERITY);
add_function (ex, "render_surface");
add_source (ex, "msrender.c");
add_long (ex, "variety type", (long) type);
return;
}
if (error()) return;
}
}
/**
* Adds an option to the current options
*
* @param array $option
* @return $this
*/
PHP_METHOD(Phalcon_Forms_Element_Select, addOption){
zval **option, *values, *tmp;
phalcon_fetch_params_ex(1, 0, &option);
PHALCON_ENSURE_IS_ARRAY(option);
values = phalcon_fetch_nproperty_this(getThis(), SL("_optionsValues"), PH_NOISY TSRMLS_CC);
ALLOC_ZVAL(tmp);
if (Z_TYPE_P(values) != IS_ARRAY) {
MAKE_COPY_ZVAL(option, tmp);
}
else {
add_function(tmp, *option, values TSRMLS_CC);
}
Z_SET_REFCOUNT_P(tmp, 0);
phalcon_update_property_this(getThis(), SL("_optionsValues"), tmp TSRMLS_CC);
RETURN_THISW();
}
struct leaf *duplicate_leaf (struct leaf *lf)
{
int j, k;
struct leaf *lf2;
struct cept *ex;
lf2 = allocate_leaf ();
if (lf2 == NULL) {
add_object (tail_cept, LEAF, "leaf");
add_function (tail_cept, "duplicate_leaf");
return(NULL);
}
lf2 -> cir = lf -> cir;
lf2 -> shape = lf -> shape;
lf2 -> type = lf -> type;
lf2 -> fac = lf -> fac;
lf2 -> side = lf -> side;
lf2 -> comp = lf -> comp;
lf2 -> input_hue = lf -> input_hue;
lf2 -> cep = lf -> cep;
lf2 -> clip_ep = lf -> clip_ep;
for (j = 0; j < 2; j++) {
lf2 -> where[j] = lf -> where[j];
lf2 -> when[j] = lf -> when[j];
for (k = 0; k < 3; k++)
lf2 -> ends[j][k] = lf -> ends[j][k];
}
for (k = 0; k < 3; k++)
lf2 -> focus[k] = lf -> focus[k];
for (k = 0; k < MAXPA; k++)
lf2 -> atmnum[k] = lf -> atmnum[k];
return (lf2);
}
/* create tori */
void create_tori (struct surface *this_srf)
{
int k;
long n_pair;
double root1, root2, distance12, squared_distance12;
double radius1, radius2, torus_radius;
double axis[3];
double *sphere1_center, *sphere2_center;
char message[MAXLINE];
struct sphere *sphere1, *sphere2;
struct neighbor *first_neighbor, *last_neighbor, *neighbor;
struct neighbor *first_neighbor2, *last_neighbor2, *neighbor2;
struct pair *pair_ptr;
struct cept *ex;
if (this_srf -> n_pair <= 0) return;
/* initialize to tmp tor array beginning */
pair_ptr = this_srf -> pair_array;
n_pair = 0;
/* loop through sphere list */
for (sphere1 = (struct sphere *) (this_srf -> head_atom); sphere1 != NULL;
sphere1 = sphere1 -> next) {
if ((first_neighbor = sphere1 -> first_neighbor) == NULL) continue;
last_neighbor = sphere1 -> last_neighbor;
/* transfer info to local variables */
sphere1_center = sphere1 -> center;
radius1 = sphere1 -> radius;
/* loop through neighbors of this sphere */
for (neighbor = first_neighbor; neighbor <= last_neighbor;
neighbor++) {
sphere2 = neighbor -> sphptr;
if (sphere1 >= sphere2) continue; /* no duplication */
/* transfer info to local variables */
sphere2_center = sphere2 -> center;
radius2 = sphere2 -> radius;
/* geometric computations for torus */
for (k = 0; k < 3; k++)
axis[k] = *(sphere2_center + k) - *(sphere1_center + k);
distance12 = norm (axis);
if (distance12 <= 0.0) {
ex = new_cept (GEOMETRY_ERROR, DEGENERACY, FATAL_SEVERITY);
add_function (ex, "create_tori");
add_source (ex, "mstorus.c");
add_message (ex, "coincident atoms");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
return;
}
squared_distance12 = distance12 * distance12;
if (squared_distance12 <= 0.0) {
ex = new_cept (GEOMETRY_ERROR, DEGENERACY, FATAL_SEVERITY);
add_function (ex, "create_tori");
add_source (ex, "mstorus.c");
add_message (ex, "coincident atoms");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
return;
}
root1 = (radius1 + radius2 + 2 * this_srf -> probe_radius) *
(radius1 + radius2 + 2 * this_srf -> probe_radius) -
squared_distance12;
if (root1 < 0.0) continue; /* sphere too far away */
root1 = sqrt (root1);
root2 = squared_distance12 - (radius1 - radius2) * (radius1 - radius2);
if (root2 < 0.0) continue; /* one sphere inside other */
root2 = sqrt (root2);
torus_radius = 0.5 * root1 * root2 / distance12;
if (torus_radius <= 0.0) continue;
/* store pointer for torus in first spheres list */
neighbor -> torptr = pair_ptr;
/* store pointer for torus in second spheres list */
first_neighbor2 = sphere2 -> first_neighbor;
last_neighbor2 = sphere2 -> last_neighbor;
for (neighbor2 = first_neighbor2;
neighbor2 <= last_neighbor2; neighbor2++)
if (neighbor2 -> sphptr == sphere1) {
neighbor2 -> torptr = pair_ptr;
break;
}
pair_ptr -> free = TRUE;
pair_ptr -> buried = TRUE;
pair_ptr -> sph[0] = sphere1;
pair_ptr -> sph[1] = sphere2;
pair_ptr++;
n_pair = pair_ptr - this_srf -> pair_array;
if (n_pair > this_srf -> n_pair) {
ex = new_cept (LOGIC_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "create_tori");
add_source (ex, "mstorus.c");
add_long (ex, "before", this_srf -> n_pair);
add_long (ex, "after", n_pair);
add_message (ex, "inconsistent number of neighbors");
return;
}
}
}
this_srf -> n_pair = n_pair;
sprintf (message, "%8ld neighbor pairs", n_pair);
inform (message);
return;
}
void setup_torus_fields (double probe_radius, struct pair *pair_ptr, double torus_center[3], double *return_radius, double torus_axis[3])
{
int k;
double root1, root2, asymmetry;
double distance12, distance12_squared;
double radius1, radius2, torus_radius;
double *sphere1_center, *sphere2_center;
char message[MAXLINE];
struct sphere *sphere1, *sphere2;
struct cept *ex;
sphere1 = pair_ptr -> sph[0];
sphere2 = pair_ptr -> sph[1];
if (sphere1 >= sphere2) {
ex = new_cept (LOGIC_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "setup_torus_fields");
add_source (ex, "mstorus.c");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
return;
}
/* transfer info to local variables */
sphere1_center = sphere1 -> center;
radius1 = sphere1 -> radius;
sphere2_center = sphere2 -> center;
radius2 = sphere2 -> radius;
/* geometric computations for torus */
for (k = 0; k < 3; k++)
torus_axis[k] = *(sphere2_center + k) - *(sphere1_center + k);
distance12 = norm (torus_axis);
if (distance12 <= 0.0) {
ex = new_cept (GEOMETRY_ERROR, DEGENERACY, FATAL_SEVERITY);
add_function (ex, "setup_torus_fields");
add_source (ex, "mstorus.c");
add_message (ex, "coincident atoms");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
return;
}
distance12_squared = distance12 * distance12;
if (distance12_squared <= 0.0) {
ex = new_cept (GEOMETRY_ERROR, DEGENERACY, FATAL_SEVERITY);
add_function (ex, "setup_torus_fields");
add_source (ex, "mstorus.c");
add_message (ex, "coincident atoms");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
return;
}
for (k = 0; k < 3; k++) torus_axis[k] /= distance12;
root1 = (radius1 + radius2 + 2 * probe_radius) *
(radius1 + radius2 + 2 * probe_radius) - distance12_squared;
if (root1 < 0.0) {
ex = new_cept (LOGIC_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "setup_torus_fields");
add_source (ex, "mstorus.c");
add_message (ex, "inconsistent existence of torus");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
add_double (ex, "root1", root1);
return;
}
root1 = sqrt (root1);
root2 = distance12_squared - (radius1 - radius2) *
(radius1 - radius2);
if (root2 < 0.0) {
ex = new_cept (LOGIC_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "setup_torus_fields");
add_source (ex, "mstorus.c");
add_message (ex, "inconsistent existence of torus");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
add_double (ex, "root2", root2);
return;
}
root2 = sqrt (root2);
torus_radius = 0.5 * root1 * root2 / distance12;
if (torus_radius <= 0) {
ex = new_cept (LOGIC_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "setup_torus_fields");
add_source (ex, "mstorus.c");
add_message (ex, "inconsistent existence of torus");
add_atom (ex, sphere1);
add_atom (ex, sphere2);
add_double (ex, "torus_radius", torus_radius);
return;
}
asymmetry = (radius1 + probe_radius) * (radius1 + probe_radius) -
(radius2 + probe_radius) * (radius2 + probe_radius);
for (k = 0; k < 3; k++)
torus_center[k] = 0.5 * (*(sphere1_center + k) +
*(sphere2_center + k))
+ 0.5 * torus_axis[k] * asymmetry / distance12;
*return_radius = torus_radius;
return;
}
/* regular saddle surfaces for this torus */
void regular_saddle (struct surface *this_srf, struct torus *torus_ptr)
{
int k, n_torus_arcs, arc_index;
int index0, index1;
struct arc *arc1, *arc2;
struct circle *circle1, *circle2;
double circle_points[MAX_SORT][3];
double point_vector1[3];
double point_vector2[3];
short arc_orn[MAX_SORT];
short indices[MAX_SORT];
struct arc **arc_list, **arc_hdl;
double wrap_angle;
struct cept *ex;
/* set up circles */
circle1 = new_contact_circle (this_srf, torus_ptr, 0); if (error()) return;
circle2 = new_contact_circle (this_srf, torus_ptr, 1); if (error()) return;
/* count arcs belonging to torus */
n_torus_arcs = 0;
for (arc1 = torus_ptr -> first_arc; arc1 != NULL;
arc1 = arc1 -> next) n_torus_arcs++;
if (n_torus_arcs <= 0) return;
/* must be even */
if (0 != n_torus_arcs % 2) {
ex = new_cept (GEOMETRY_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "regular_saddle");
add_source (ex, "msface.c");
add_long (ex, "n_torus_arcs", n_torus_arcs);
add_atom (ex, torus_ptr -> atm[0]);
add_atom (ex, torus_ptr -> atm[1]);
add_message (ex, "odd number of torus arcs");
return;
}
if (n_torus_arcs > MAX_SORT) {
ex = new_cept (GEOMETRY_ERROR, MSOVERFLOW, FATAL_SEVERITY);
add_function (ex, "regular_saddle");
add_source (ex, "msface.c");
add_long (ex, "n_torus_arcs", n_torus_arcs);
add_long (ex, "MAX_SORT", MAX_SORT);
add_atom (ex, torus_ptr -> atm[0]);
add_atom (ex, torus_ptr -> atm[1]);
return;
}
/* allocate memory */
arc_list = (struct arc **)
allocate_pointers (ARC, n_torus_arcs);
if (arc_list == NULL) {
ex = new_cept (MEMORY_ERROR, ALLOCATION, FATAL_SEVERITY);
add_function (ex, "regular_saddle");
add_source (ex, "msface.c");
add_atom (ex, torus_ptr -> atm[0]);
add_atom (ex, torus_ptr -> atm[1]);
return;
}
/* set up torus arc pointer list */
for (arc1 = torus_ptr -> first_arc, arc_index = 0;
arc_index < n_torus_arcs;
arc1 = arc1 -> next, arc_index++) {
arc_hdl = arc_list + arc_index;
*arc_hdl = arc1; /* pointer to arc */
}
setup_torus_arcs (torus_ptr -> axis, n_torus_arcs, arc_list,
circle_points, arc_orn);
if (error()) return;
sort_points (torus_ptr -> center, torus_ptr -> radius,
torus_ptr -> axis, n_torus_arcs, circle_points,
arc_orn, indices);
if (error()) return;
for (arc_index = 0; arc_index < n_torus_arcs; arc_index += 2) {
index0 = indices[arc_index];
arc_hdl = arc_list + index0;
arc1 = *arc_hdl;
index1 = indices[arc_index+1];
arc_hdl = arc_list + index1;
arc2 = *arc_hdl;
/* compute saddle wrap angle */
for (k = 0; k < 3; k++) {
point_vector1[k] =
(circle_points[index0][k] - torus_ptr -> center[k]) /
torus_ptr -> radius;
point_vector2[k] =
(circle_points[index1][k] - torus_ptr -> center[k]) /
torus_ptr -> radius;
}
wrap_angle = positive_angle (point_vector1, point_vector2,
torus_ptr -> axis);
/* create saddle face */
newsad (this_srf, arc1, arc2, circle1, circle2, torus_ptr, wrap_angle);
if (error()) return;
}
/* free temporary memory */
free_pointers (ARC, arc_list);
}
